Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

[whitneyt1]

Hello!

I am trying to run DEG function with method="DESeq2" between three groups for single cell RNA seq data.

deg_BcellsM<-DEG(data %>% filter(cell_type=='B-cells-M'),method='DESeq2',contrast=c("grouped_pd","grouped_pr","naive"))
but am getting the following output:

Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

My data file contains the columns as gene names + cell_type and compare_group columns, and the rows are each individual single cell. My groups are named 'grouped_pr', 'grouped_pd', 'naive'.

Do you have any advice on how to proceed?

Thank you!

[ywang65]

It seems like your input data are not integers. While DESeq2 requires raw counts as input. You can find more info about DESeq2 here https://bioc.ism.ac.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf

…

________________________________ From: whitneyt <[email protected]> Sent: Wednesday, April 22, 2020 12:44:56 PM To: Coolgenome/iTALK Cc: Subscribed Subject: [Coolgenome/iTALK] Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers (#15) **** EXTERNAL EMAIL **** Hello! I am trying to run DEG function with method="DESeq2" between three groups for single cell RNA seq data. deg_BcellsM<-DEG(data %>% filter(cell_type=='B-cells-M'),method='DESeq2',contrast=c("grouped_pd","grouped_pr","naive")) but am getting the following output: Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers My data file contains the columns as gene names + cell_type and compare_group columns, and the rows are each individual single cell. Do you have any advice on how to proceed? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Coolgenome_iTALK_issues_15&d=DwMFaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=rToYrokj6a4BSRlGOUeu519hfbAHJ_4tfwHbADc3H0Q&m=jeBzATMKeNDbRiA7V9VsGVYK0cevYnBiHGbZy5nCoZ4&s=F2y9IRLaQ-fnNDjDYXKtmOOH8B8kCdX7avfj8kuXkU8&e=>, or unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AKTJNZUOHFJQN7LZ2DW43VTRN4UJRANCNFSM4MOL25ZA&d=DwMFaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=rToYrokj6a4BSRlGOUeu519hfbAHJ_4tfwHbADc3H0Q&m=jeBzATMKeNDbRiA7V9VsGVYK0cevYnBiHGbZy5nCoZ4&s=UpZSPwCLklaB5qLZCSjI-h1Z-szWHEr6u26CAOK7bA0&e=>.